Shiny side up - always, although Epson say you should do it emulsion side up. It matters not if it is colour, B&W negs or transparencies. That is according to Epson, but it is a simple matter with the preview thumbnails to flip them over.
You got me thinking and I scanned a B&W negative with ICE and without. With the one that employed ICE, it was was dreadful! The edges of some objects were all broken up and 'mushy' more or less the same as you get with the Nikon Scanner. The other one was OK-ish but not as good as the Nikon.
AS Matt mentions, are there different editions of ICE? With the Nikon version that is around18 years old, likewise with Minilab scanner where they have ICE. The one in my V600 will be possibly only 3-4 years old although I have owned this scanner for less than a year.